SMTL ID : 9cao.1

Aminopeptidase N open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

5 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: D.433, L.624, N.625, I.656 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: S.84, Y.85, R.86, T.108, R.110, N.234, T.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.110, A:R.110 NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: K.241, L.243, S.255, P.257, N.265 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 7 residues within 4Å: Chain A: E.636, R.640, Q.643, P.675, T.677, L.678, N.681 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 5 residues within 4Å: Chain B: D.433, Q.596, L.624, N.625, I.656 No protein-ligand interaction detected (PLIP)

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.5: 3 residues within 4Å: Chain A: D.315, Y.316, N.319 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: L.100, V.102, N.128, E.183, G.184, E.185 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain B: N.96, R.98, L.100, V.102, N.128, E.183 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.98 Hydrogen bonds: B:R.98 NAG-NAG.8: 8 residues within 4Å: Chain B: S.84, Y.85, R.86, R.110, Q.175, E.177, N.234, T.271 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.110, B:R.110 NAG-NAG.9: 6 residues within 4Å: Chain B: E.636, P.675, T.677, L.678, N.681, L.684 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain B: D.315, Y.316, N.319, F.369, P.371 No protein-ligand interaction detected (PLIP)

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.12: 2 residues within 4Å: Chain A: N.527, S.529 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.527 NAG.13: 2 residues within 4Å: Chain A: N.784, N.818 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.818 NAG.15: 8 residues within 4Å: Chain B: H.239, K.241, D.242, L.243, T.244, S.255, P.257, N.265 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.241, B:S.255, B:N.265 NAG.16: 1 residues within 4Å: Chain B: N.527 No protein-ligand interaction detected (PLIP) NAG.17: 1 residues within 4Å: Chain B: N.818 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.14: 5 residues within 4Å: Chain A: E.355, H.388, E.389, H.392, E.411 No protein-ligand interaction detected (PLIP) ZN.18: 5 residues within 4Å: Chain B: E.355, H.388, E.389, H.392, E.411 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.392, B:E.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lyu, M. et al., Aminopeptidase N open state. To Be Published

Release Date

2025-08-06

Peptides

Aminopeptidase N: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Aminopeptidase N

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